It seems that there was a disconnect or upheaval of some kind between the times of the Geonim and the times of the Rishonim and the hakhamim that these two eras contained. Shittoth regarding tefila, berakhoth, kashruth, and other areas seem to have been practiced in a completely different manner until many Rishonim came along and views things differently.

My question is: "What happened? How their understanding of halakha be so different? Further, how could the Gemara and other literature be viewed so differently between them?"

@ShmuelBrin - Actually, the Rambam does not hold this way at all and regularly ignores Gaonic legislation not found in the Talmudic literature. See his Haqdama to the Mishne Tora where he rejects the idea of "halakha k'bathra'ei." Kol tuv.
– user3342Dec 10 '13 at 4:01

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@SethJ - Tefila = look in the Sidurim of Rasa"G, Rav Amram, and the teshuvoth of Rav Nattronai. You will see berakhoth - with she and malkhuth - which were said regularly, but were later understood by the Rishonim to be berakhoth l'vattala. Berakhoth = see above, but specifically berakhoth were "innovated" after the Sanhedrin by the Geonim, but later ruled to be "asur" to say. Kashruth = Rules of Sh'hitta, Rav Qapah notes in his pirush on the Rambam that halitta seems to have been required by the Gaonim, but not by Rishonim - almost universally. Hope this helps. Kol tuv.
– user3342Dec 10 '13 at 4:07

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@Maimonist did the rif require it? i know ravad was harsh on him bout it. and most others dont hold like him. but i never seen the rif mentioning it either
– MoriDowidhYa3aqovDec 10 '13 at 5:00

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@MoriDoweedhYaa3gob - the point is that Mori Yusuf z"l had no source (he admits this in that section) on which to base his assumption. But seeing that the Rambam required it while all others did not made him think that the Rambam was continuing a Geonic injunction while the other Rishonim had abandoned it. The fact is that the Gemara before us mentions NOTHING of halitta except for livers and other bloody organs, but never regular cuts of meat, and certainly not poultry. Kol tuv.
– user3342Dec 10 '13 at 5:03